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Wireless communications over water may suffer from serious multipath fading due to strong specular reflections from conducting water surfaces. Cognitive radios enable dynamic spectrum access over a large frequency range, which can be used to mitigate this problem. In this paper, we study how to leverage cognitive radios for effective communications in wireless networks over water. We formally define the related problem as the Overwater Channel Scheduling Problem (OCSP) which seeks a channel assignment schedule such that a "good" communication link can be maintained between every Mobile Station (MS) and the Base Station (BS) all the time. We present a general scheduling framework for solving the OCSP. Based on the proposed framework, we present an optimal algorithm and several fast heuristic algorithms. In addition, we discuss an extension to the heavy traffic load case and propose two throughput-aware scheduling algorithms. We performed simulation runs based on path loss data provided by the Advanced Refractive Effects Prediction System (AREPS) and present simulation results to justify the efficiency of the proposed scheduling algorithms.